def test_comparison(self):
alignment = self.alignment
self.assertEqual(alignment.shape, (7, 156))
sequences = alignment.sequences
coordinates = numpy.array(alignment.coordinates)
other = Align.Alignment(sequences, coordinates)
self.assertEqual(alignment, other)
self.assertLessEqual(alignment, other)
self.assertGreaterEqual(other, alignment)
other = Align.Alignment(sequences, coordinates[:, 1:])
self.assertNotEqual(alignment, other)
self.assertLess(alignment, other)
self.assertLessEqual(alignment, other)
self.assertGreater(other, alignment)
self.assertGreaterEqual(other, alignment)
def test_target_query_properties(self):
target = "ABCD"
query = "XYZ"
sequences = [target, query]
coordinates = numpy.array([[0, 3, 4], [0, 3, 3]])
alignment = Align.Alignment(sequences, coordinates)
self.assertEqual(alignment.sequences[0], target)
self.assertEqual(alignment.sequences[1], query)
self.assertEqual(alignment.target, target)
self.assertEqual(alignment.query, query)
target = "EFGH"
query = "UVW"
sequences = [target, query]
alignment.sequences = sequences
self.assertEqual(alignment.sequences[0], target)
self.assertEqual(alignment.sequences[1], query)
self.assertEqual(alignment.target, target)
self.assertEqual(alignment.query, query)
target = "IJKL"
query = "RST"
sequences = [target, query]
alignment.sequences = sequences
self.assertEqual(alignment.sequences[0], target)
self.assertEqual(alignment.sequences[1], query)
self.assertEqual(alignment.target, target)
self.assertEqual(alignment.query, query)
def test_indexing_slicing(self):
target = "AACCGGGACCG"
query = "ACGGAAC"
sequences = (target, query)
coordinates = numpy.array([[0, 1, 2, 3, 4, 6, 7, 8, 8, 9, 11],
[0, 1, 1, 2, 2, 4, 4, 5, 6, 7, 7]])
alignment = Align.Alignment(sequences, coordinates)
alignment.score = 6.0
msg = "forward strand"
self.check_indexing_slicing(alignment, msg)
query = reverse_complement(query)
sequences = (target, query)
coordinates = numpy.array([[0, 1, 2, 3, 4, 6, 7, 8, 8, 9, 11],
[7, 6, 6, 5, 5, 3, 3, 2, 1, 0, 0]])
alignment = Align.Alignment(sequences, coordinates)
alignment.score = 6.0
msg = "reverse strand"
self.check_indexing_slicing(alignment, msg)
def test_indexing_slicing(self):
target = "AACCGGGACCG"
query = "ACGGAAC"
query_rc = reverse_complement(query)
sequences = (target, query)
forward_coordinates = numpy.array([[0, 1, 2, 3, 4, 6, 7, 8, 8, 9, 11],
[0, 1, 1, 2, 2, 4, 4, 5, 6, 7, 7]])
alignment = Align.Alignment(sequences, forward_coordinates)
alignment.score = 6.0
msg = "str, forward strand"
self.check_indexing_slicing(alignment, msg)
sequences = (target, query_rc)
reverse_coordinates = numpy.array([[0, 1, 2, 3, 4, 6, 7, 8, 8, 9, 11],
[7, 6, 6, 5, 5, 3, 3, 2, 1, 0, 0]])
alignment = Align.Alignment(sequences, reverse_coordinates)
alignment.score = 6.0
msg = "str, reverse strand"
self.check_indexing_slicing(alignment, msg)
target = Seq(target)
query = Seq(query)
query_rc = Seq(query_rc)
sequences = (target, query)
alignment = Align.Alignment(sequences, forward_coordinates)
alignment.score = 6.0
msg = "Seq, forward strand"
self.check_indexing_slicing(alignment, msg)
sequences = (target, query_rc)
alignment = Align.Alignment(sequences, reverse_coordinates)
alignment.score = 6.0
msg = "Seq, reverse strand"
self.check_indexing_slicing(alignment, msg)
target = SeqRecord(target)
query = SeqRecord(query)
query_rc = SeqRecord(query_rc)
sequences = (target, query)
alignment = Align.Alignment(sequences, forward_coordinates)
alignment.score = 6.0
msg = "SeqRecord, forward strand"
self.check_indexing_slicing(alignment, msg)
sequences = (target, query_rc)
alignment = Align.Alignment(sequences, reverse_coordinates)
alignment.score = 6.0
msg = "SeqRecord, reverse strand"
self.check_indexing_slicing(alignment, msg)
def test_substitutions(self):
path = os.path.join("Align", "ecoli.fa")
record = SeqIO.read(path, "fasta")
target = record.seq
path = os.path.join("Align", "bsubtilis.fa")
record = SeqIO.read(path, "fasta")
query = record.seq
coordinates = numpy.array([
[
503,
744,
744,
747,
748,
820,
820,
822,
822,
823,
823,
828,
828,
833,
833,
845,
848,
850,
851,
854,
857,
1003,
1004,
1011,
1011,
1017,
1017,
1020,
1021,
1116,
1116,
1119,
1120,
1132,
1133,
1242,
1243,
1246,
1246,
1289,
1289,
1292,
1293,
1413,
],
[
512,
753,
754,
757,
757,
829,
831,
833,
834,
835,
838,
843,
844,
849,
850,
862,
862,
864,
864,
867,
867,
1013,
1013,
1020,
1021,
1027,
1028,
1031,
1031,
1126,
1127,
1130,
1130,
1142,
1142,
1251,
1251,
1254,
1255,
1298,
1299,
1302,
1302,
1422,
],
])
sequences = (target, query)
forward_alignment = Align.Alignment(sequences, coordinates)
sequences = (target, query.reverse_complement())
coordinates = coordinates.copy()
coordinates[1, :] = len(query) - coordinates[1, :]
reverse_alignment = Align.Alignment(sequences, coordinates)
for alignment in (forward_alignment, reverse_alignment):
m = alignment.substitutions
self.assertEqual(
str(m),
"""\
A C G T
A 191.0 3.0 15.0 13.0
C 5.0 186.0 9.0 14.0
G 12.0 11.0 248.0 8.0
T 11.0 19.0 6.0 145.0
""",
)
self.assertAlmostEqual(m["T", "C"], 19.0)
self.assertAlmostEqual(m["C", "T"], 14.0)
m += m.transpose()
m /= 2.0
self.assertEqual(
str(m),
"""\
A C G T
A 191.0 4.0 13.5 12.0
C 4.0 186.0 10.0 16.5
G 13.5 10.0 248.0 7.0
T 12.0 16.5 7.0 145.0
""",
)
self.assertAlmostEqual(m["C", "T"], 16.5)
self.assertAlmostEqual(m["T", "C"], 16.5)
def test_sort(self):
target = Seq("ACTT")
query = Seq("ACCT")
sequences = (target, query)
coordinates = numpy.array([[0, 4], [0, 4]])
alignment = Align.Alignment(sequences, coordinates)
self.assertEqual(
str(alignment),
"""\
ACTT
||.|
ACCT
""",
)
alignment.sort()
self.assertEqual(
str(alignment),
"""\
ACCT
||.|
ACTT
""",
)
alignment.sort(reverse=True)
self.assertEqual(
str(alignment),
"""\
ACTT
||.|
ACCT
""",
)
target.id = "seq1"
query.id = "seq2"
alignment.sort()
self.assertEqual(
str(alignment),
"""\
ACTT
||.|
ACCT
""",
)
alignment.sort(reverse=True)
self.assertEqual(
str(alignment),
"""\
ACCT
||.|
ACTT
""",
)
alignment.sort(key=GC)
self.assertEqual(
str(alignment),
"""\
ACTT
||.|
ACCT
""",
)
alignment.sort(key=GC, reverse=True)
self.assertEqual(
str(alignment),
"""\
ACCT
||.|
ACTT
""",
)
